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revision 1.10 by cnh, Thu Apr 6 20:03:45 2006 UTC revision 1.37 by cnh, Wed Jun 28 15:11:42 2006 UTC
# Line 1  Line 1 
1    Editors
2    
3     Overall       - JM, AM, PH, CNH, EH3
4    
5     Front content - EH3
6    
7     Chapter 1     - CNH
8    
9     Chapter 2     - JMC
10    
11     Chapter 3     -  AM
12    
13     Chapter 4     - CNH
14    
15     Chapter 5     -  PH
16    
17     Chapter 6     -  AM
18    
19     Chapter 7     - EH3
20    
21     Chapter 8     -  PH
22    
23     Chapter 9     - CNH (Applications)
24    
25     Chapter 10    - JMC (Under development chapter)
26    
27     Biblio        - EH3
28    
29  Rebuild and set to do cron build - DONE on hugo  Rebuild and set to do cron build - DONE on hugo
30    
31  To do  To do
# Line 8  To do Line 36  To do
36      Add an "Under development, chapter" - shortish description of what      Add an "Under development, chapter" - shortish description of what
37      is available (last chapter)      is available (last chapter)
38    
39      - add in example latex for formatting author names in different pieces.
40        this aknowledges peoples contributions and gives ref for who
41        to talk to.
42    
43  o HTML, scripts and front content  o HTML, scripts and front content
44    
45    - pick a URL    - pick a URL
46      TBD      TBD
47    
   - mitgcm.org very front page.  
     o too many clicks to get to model manual.  
       make doc link go to mitgcm.org/r2_web_testing/latest  
       and add "HowTo" reference etc... to /latest page  
   
48    - mitgcm.org/r2_web_testing/latest    - mitgcm.org/r2_web_testing/latest
49      o add another short-cut for quick download      o add another short-cut for quick download
50    
# Line 30  o HTML, scripts and front content Line 56  o HTML, scripts and front content
56        Tutorials (broken)        Tutorials (broken)
57        Browse Code        Browse Code
58    
     o mitgcm.org (front content) [DONE]  
       Get Code (where does this go to?)  
       get rid of * CVS current bullet  
       make HTML-enabled CVS code browser leap to MITgcm/MITgcm  
   
     o authors  
       John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen,  
       Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos,  
       Gael - others?  
   
59      o words on http://mitgcm.org/r2_web_testing/latest      o words on http://mitgcm.org/r2_web_testing/latest
60        change to        change to
61         "access on-line Auser manual/A and Atable of contents/A         "access on-line Auser manual/A and Atable of contents/A
# Line 72  o Latex Line 88  o Latex
88    
89        o List of key papers needs to be updated and reformatted        o List of key papers needs to be updated and reformatted
90    
   
91        o Global atmosphere: `Held Suarez',        o Global atmosphere: `Held Suarez',
92          update Adcroft reference          update Adcroft reference
93          fix up ingrid link and frame (ingrid movies seem to be broken?)          fix up ingrid link and frame (ingrid movies seem to be broken?)
# Line 298  in content: Horizontal Dissipation: 2 ti Line 313  in content: Horizontal Dissipation: 2 ti
313    to add: mention the angle of the grid direction relative to    to add: mention the angle of the grid direction relative to
314    Eastward, Northward direction.    Eastward, Northward direction.
315    + mention horizGridFile= in file "data" (PARM04)    + mention horizGridFile= in file "data" (PARM04)
316  - add cylindrical grid description  - add cylindrical polar grid description
317     need to do a better job of relating model variables to this diagram     need to do a better job of relating model variables to this diagram
318    
319    
# Line 325  in content: Horizontal Dissipation: 2 ti Line 340  in content: Horizontal Dissipation: 2 ti
340      o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags      o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
341        in code need to explain why cos()3/2 turns out to be        in code need to explain why cos()3/2 turns out to be
342        scaling (not cos()2)        scaling (not cos()2)
343     - need to reference the smag/leith section.
344    
345  2.13.6 Vertical dissipation  2.13.6 Vertical dissipation
346   - mention the implicit vertical viscosity option and ref to section 2.5   - mention the implicit vertical viscosity option and ref to section 2.5
# Line 343  in content: Horizontal Dissipation: 2 ti Line 359  in content: Horizontal Dissipation: 2 ti
359    
360  2.16 & 2.17 & 2.18 :  2.16 & 2.17 & 2.18 :
361   - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options   - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
362     - fix equations 2.202 & 2.203 (thanks to Martin)
363    
364  2.20.2 mercator, non-dimensional Equations:  2.20.2 mercator, non-dimensional Equations:
365  - does not use std notation  - does not use std notation
366  - would be better as an appendix of section 2.20:  - would be better as an appendix of section 2.20:
367  (e.g changing the tile to:  (e.g changing the tile to:
368    - talk to Baylor
369   Appendix: non-dimensional Equations on Spherical-Polar grid.)   Appendix: non-dimensional Equations on Spherical-Polar grid.)
370    
 JM  
   
 >>>> From Ed  
371    
372  Here are the remaining bits for Chap 4 :  Diagrams of grid locations etc.... and what variables and output files
373    and/or netcdf variable names are not very easy to figure out and follow.
374   - The grammar/flow could still use some work.  Boo was an English  It would be good to redo and extend these diagrams and align with GRID.h
375     major and has experience editing/proofing technical papers.  I  content.
376     could print out a copy and ask her to read it and suggest  
    improvements.  
   
  - missing references (if you point me towards URLs, I'll add them  
    to the bibliography):  
      \ref{ref hoe and hill, ecmwf}  
      \ref{magicgarden}  
      \ref{IBMLAPI}  
      \ref{Memorychannel}  
      \ref{hoe-hill:99}  
   
  - There are a few empty sub-sections at the end of Chap 4 that  
    should either be commented out or fleshed out.  
   
 and thats about it for Chap 4.  
   
   
 Add more to quick links on front page  
   
 Chapter 6  
   
    the master package diagram does not appear in the document  
   
    pkg/ptracers doesn't seem to have any documentation (see packages list below)  
   
   
 Master list of packages (add this to beginning of chap 6)  
   
 admtlm/               - autodiff (chapter 5)  
 aim/                  - retired  
 aim_compon_interf/    - 6.6 (no content yet)  
 aim_ocn_coupler/      - 6.6 (no content yet)  
 aim_v23/              - 6.4.1 (content needs fixing - JM to do)  
 atm_common/           - 6.6 (no content yet)  
 autodiff/             - autodiff (chapter 5)  
 bulk_force/           - 6.3.3  
 cal/                  - 6.3.5  
 cd_code/              - chapter 2 (JM check)  
 cfc/                  - not sure  
 chronos/              - AM to check  
 compon_communic/      - 6.6 (no content yet)  
 cost/                 - not sure, check with PH  
 ctrl/                 - not sure, check with PH  
 debug/                - JM may do something in chapter 7 (utilities)  
 diagnostics/          - 7.1  
 dic/                  - 6.7.2  
 ebm/                  - not sure  
 ecco/                 - chapter 8  
 embed_files/          - add something to chapter 7  
 ex3/                  - rename to exch3  
 exch2/                - 6.2.2  
 exf/                  - 6.3.4  
 fizhi/                - 6.4.3  
 flt/                  - in chapter 2 (JM check)  
 gchem/                - 6.7.1  
 generic_advdiff/      - in chapter 2 (JM check)  
 ggl90/                - nothing, (Martin?)  
 gmredi/               - in chapter 2 (JM check). also need  
                         Ferrari & Mc tapering  
 grdchk/               - grdchk (chapter 5 - check with PH)  
 gridalt/              - 6.2.4  
 kpp/                  - 6.3.2  
 land/                 - 6.4.2 (not connected to code - JM to fix)  
 matrix/               - Samar  
 mdsio/                - 7.3.1  
 mnc/                  - 7.2.1  
 mom_common/           - in chapter 2 (JM check)  
 mom_fluxform/         - in chapter 2 (JM check)  
 mom_vecinv/           - in chapter 2 (JM check)  
 monitor/              - 7.4  
 my82/                 - nothing, (martin?)  
 obcs/                 - 6.3 (needs a check)  
 ocn_compon_interf/    - 6.6 (no content yet)  
 offline/              - nothing, tutorials that need work but no package   section entry  
 opps/                 - nothing, (martin?)  
 pp81/                 - nothing, (martin?)  
 profiles/             - GAEL  
 ptracers/             - JM + SD to write something  
 rbcs/                 - talk to steph  
 runclock/             - runclock  
 rw/                   - not sure  
 sbo/                  - text in sbo_descruption.tex but not linked into  
                         part6  
 seaice/               - 6.5.2 - no equations, dimitris has promised some  
 shap_filt/            - chapter 2, JM to check  
 shelfice/             - nothing yet (martin?)  
 solver/               - empty  
 sphere/               - chapter 5 or 8 (PH to check)  
 therm_seaice/         - empty  
 thsice/               - 6.5.1 (JM to update?)  
 timeave/              - retiring......  
 zonal_filt/           - chapter 2 (JM to check)  
   
 Possible for chap 7 - Daniels grafix/ stuff  
   
 Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started.  
   
 Figure 6.8 is missing  
   
 6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997  
  Figure 6.8 is missing  
   
   
 >>>> From Andrea  
   
 to do list for chap 7:  
   
   
 7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu"  
         the links are pointing to the proper place  
   
 7.5.1 - add Graphix to the list of stuff in utils/matlab  
 7.5.2 - empty  
377    
378    JM
379    
 andrea  
380    
381  >>>> From Andrea  >>>> From Andrea
382    
# Line 482  Chapter 3 Line 385  Chapter 3
385    
386  Almost all of the 'math mode' text is dropped down as subscripts  Almost all of the 'math mode' text is dropped down as subscripts
387    
 divide chapter 3 more clearly into 2 sections?  
    (ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and  
     then 3.19 and 3.20 are informational again - rearrange subsections?)  
   
388  3.1 - don't need a link to the outside of the document (remove it)  3.1 - don't need a link to the outside of the document (remove it)
389      - link to htdig is broken      - link to htdig is broken
390    
# Line 531  divide chapter 3 more clearly into 2 sec Line 430  divide chapter 3 more clearly into 2 sec
430          are written.          are written.
431  3.6.1.2 - needs to be moved to inside section 3.6.2  3.6.1.2 - needs to be moved to inside section 3.6.2
432    
 3.7 - this section is superfluous - remove it -OR- put the tutorial sections (3.8-3.18)  
       underneath this one and leave the text for 3.7 in place  
   
433  All the 'overview' sections need some reference to the name of the experiment in  All the 'overview' sections need some reference to the name of the experiment in
434  the verification directory  the verification directory
435    
# Line 570  the verification directory Line 466  the verification directory
466       offline - duplicate inputs, what is it, tidy up cfc v.       offline - duplicate inputs, what is it, tidy up cfc v.
467                 other offline. JM thinks these need tidying up.                 other offline. JM thinks these need tidying up.
468    
469    Which of the following are which tutorial?
470    adjustment.128x64x1
471    adjustment.cs-32x32x1
472    advect_cs
473    advect_xy
474    advect_xz
475    aim.5l_cs
476    aim.5l_Equatorial_Channel
477    aim.5l_LatLon
478    biogeo
479    bottom_ctrl_5x5
480    cfc_example
481    cpl_aim+ocn
482    dome
483    exp2
484    exp4
485    exp5
486    fizhi-cs-32x32x10
487    fizhi-cs-aqualev20
488    fizhi-gridalt-hs
489    flt_example
490    front_relax
491    global1x1_tot
492    global2x2_tot
493    global_ocean.90x40x15
494    global_ocean.cs32x15
495    global_ocean.cubed32x32x30
496    global_ocean_ebm
497    global_with_exf
498    hs94.128x64x5
499    hs94.1x64x5
500    hs94.cs-32x32x5
501    ideal_2D_oce
502    internal_wave
503    inverted_barometer
504    lab_sea
505    matrix_example
506    MLAdjust
507    natl_box
508    natl_box_adjoint
509    OpenAD
510    rotating_tank
511    solid-body.cs-32x32x1
512    tidal_basin_2d
513    tutorial_baroclinic_gyre
514    tutorial_barotropic_gyre
515    tutorial_cfc_offline
516    tutorial_deep_convection
517    tutorial_global_oce_biogeo
518    tutorial_global_oce_in_p
519    tutorial_global_oce_latlon
520    tutorial_global_oce_optim
521    tutorial_held_suarez_cs
522    tutorial_offline
523    tutorial_plume_on_slope
524    tutorial_tracer_adjsens
525    vermix
526    
527    >>>> From Ed
528    
529    Here are the remaining bits for Chap 4 :
530    
531     - missing references (if you point me towards URLs, I'll add them
532       to the bibliography):
533         \ref{ref hoe and hill, ecmwf}
534         \ref{magicgarden}
535         \ref{IBMLAPI}
536         \ref{Memorychannel}
537         \ref{hoe-hill:99}
538    
539     - There are a few empty sub-sections at the end of Chap 4 that
540       should either be commented out or fleshed out.
541    
542    and thats about it for Chap 4.
543    
544    
545    Add more to quick links on front page
546    
547    Chapter 6
548    
549       the master package diagram does not appear in the document
550    
551    Master list of packages (add this to beginning of chap 6)
552    
553    admtlm/               - autodiff (chapter 5)
554    aim/                  - retired
555    aim_compon_interf/    - 6.6 (no content yet)(Daniel + JM)
556    aim_ocn_coupler/      - 6.6 (no content yet)
557    aim_v23/              - 6.4.1 (content needs fixing - JM to do)
558    atm_common/           - nothing in this package (6.4.1 related)
559    autodiff/             - autodiff (chapter 5)
560    bulk_force/           - 6.3.3
561    cal/                  - 6.3.5
562    cd_code/              - chapter 2 (JM check add a reference to paper,
563                              mention parameter in data)
564    cfc/                  - not sure  (CNH to talk to Steph and Helen)
565    chronos/              - AM to check (not being used - Andrea to kill it)
566    compon_communic/      - 6.6 (no content yet)(Daniel + JM)
567    cost/                 - not sure, check with PH
568    ctrl/                 - not sure, check with PH
569    debug/                - JM may do something in chapter 7 (utilities)
570    diagnostics/          - 7.1
571    dic/                  - 6.7.2
572    ebm/                  - (check with PH)
573    ecco/                 - chapter 8
574    embed_files/          - add something to chapter 7
575    exch2/                - 6.2.2
576    exf/                  - 6.3.4
577    fizhi/                - 6.4.3
578    flt/                  - (PH check)
579    gchem/                - 6.7.1
580    generic_advdiff/      - in chapter 2 (JM check)
581    ggl90/                - nothing, (Martin?)
582    gmredi/               - in chapter 2 (JM check). also need
583                            Ferrari & Mc transition zone stuff (Samar doing this)
584                            get dfer to read this
585    grdchk/               - grdchk (chapter 5 - check with PH)
586    gridalt/              - 6.2.4
587    kpp/                  - 6.3.2
588    land/                 - 6.4.2 (not connected to code Rong's notes - JM to fix)
589    matrix/               - Samar
590    mdsio/                - 7.3.1
591    mnc/                  - 7.2.1
592    mom_common/           - in chapter 2 (JM check)
593    mom_fluxform/         - in chapter 2 (JM check)
594    mom_vecinv/           - in chapter 2 (JM check)
595    monitor/              - 7.4
596    my82/                 - nothing, (martin?)
597    obcs/                 - 6.3 (needs a check - ask PH to read)
598    ocn_compon_interf/    - 6.6 (no content yet)
599    offline/              - nothing, tutorials that need work but no package   section entry
600                            trivial to document (CNH to do)
601    opps/                 - nothing, (martin?)
602    pp81/                 - nothing, (martin?)
603    profiles/             - GAEL
604    ptracers/             - JM + SD + Martin to write something (nothing for this
605                              at the moment)
606                            AM has diagnostics table for this.
607    rbcs/                 - CNH to talk to steph
608    runclock/             - runclock - CNH
609    rw/                   - not sure - going to stay says JMC. quick IO calls
610                            JMC to write a quick note for that.
611    sbo/                  - text in sbo_descruption.tex but not linked into
612                            part6 - CNH
613    seaice/               - 6.5.2 - no equations, dimitris has promised some
614    shap_filt/            - chapter 2, JM to check
615    shelfice/             - nothing yet (martin?)
616    solver/               - empty (go away?)
617    sphere/               - chapter 5 or 8 (PH to check)
618    therm_seaice/         - empty (go away?)
619    thsice/               - 6.5.1 (JM to update?)
620    timeave/              - retiring......
621    zonal_filt/           - chapter 2 (JM to check)
622    
623    list an expeiment which uses package? CNH
624    
625    6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
626     Figure 6.8 is missing
627    
628    
629    =====  Chapter 7  =====  [EH3 editing] :
630    
631    7.1.x - JMC: please add description of:
632            - diagstat
633            - new temporal averaging feature
634    
635  9. Model uses  7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel)
636    
637    7.5.2 - get bathymetry pre-processing stuff from Patrick
638            and then describe it
639    
640    add something on spgrid mesh generator (maybe)?
641    
642    
643    andrea
644    
645    
646    9. Publications using MITgcm --> "Previous Applications of MITgcm"
647     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
648     (check in support for more names)     (check in support for more names)
649    
650    10. Under development
651    
652    Constantinos LCML
653    
654    
655    Bibliography
656    
657     tidy up from misc - .tex
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